WntConcentration.cpp

/*

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*/
#include "WntConcentration.hpp"

template<unsigned DIM>
WntConcentration<DIM>* WntConcentration<DIM>::mpInstance = NULL;

template<unsigned DIM>
WntConcentration<DIM>* WntConcentration<DIM>::Instance()
{
    if (mpInstance == NULL)
    {
        mpInstance = new WntConcentration;
    }
    return mpInstance;
}

template<unsigned DIM>
WntConcentration<DIM>::WntConcentration()
    : mCryptLength(DOUBLE_UNSET),
      mLengthSet(false),
      mWntType(NONE),
      mpCellPopulation(NULL),
      mTypeSet(false),
      mConstantWntValueForTesting(0),
      mUseConstantWntValueForTesting(false),
      mWntConcentrationParameter(1.0),
      mCryptProjectionParameterA(0.5),
      mCryptProjectionParameterB(2.0)
{
    // Make sure there's only one instance - enforces correct serialization
    assert(mpInstance == NULL);
}

template<unsigned DIM>
WntConcentration<DIM>::~WntConcentration()
{
}

template<unsigned DIM>
void WntConcentration<DIM>::Destroy()
{
    if (mpInstance)
    {
        delete mpInstance;
        mpInstance = NULL;
    }
}

template<unsigned DIM>
double WntConcentration<DIM>::GetWntLevel(CellPtr pCell)
{
    if (mUseConstantWntValueForTesting)  // to test a cell and cell-cycle models without a cell population
    {
        return mConstantWntValueForTesting;
    }

    assert(mpCellPopulation!=NULL);
    assert(mTypeSet);
    assert(mLengthSet);

    double height;

    if (mWntType == RADIAL)
    {
        double a = GetCryptProjectionParameterA();
        double b = GetCryptProjectionParameterB();
        height = a*pow(norm_2(mpCellPopulation->GetLocationOfCellCentre(pCell)), b);
    }
    else
    {
        height = mpCellPopulation->GetLocationOfCellCentre(pCell)[DIM-1];
    }

    return GetWntLevel(height);
}

template<unsigned DIM>
c_vector<double, DIM> WntConcentration<DIM>::GetWntGradient(CellPtr pCell)
{
    if (mUseConstantWntValueForTesting)  // to test a cell and cell-cycle models without a cell population
    {
        return zero_vector<double>(DIM);
    }
    assert(mpCellPopulation!=NULL);
    assert(mTypeSet);
    assert(mLengthSet);

    c_vector<double, DIM> location_of_cell = mpCellPopulation->GetLocationOfCellCentre(pCell);

    return GetWntGradient(location_of_cell);
}

template<unsigned DIM>
void WntConcentration<DIM>::SetCellPopulation(AbstractCellPopulation<DIM>& rCellPopulation)
{
    mpCellPopulation = &rCellPopulation;
}

template<unsigned DIM>
AbstractCellPopulation<DIM>& WntConcentration<DIM>::rGetCellPopulation()
{
    return *mpCellPopulation;
}

template<unsigned DIM>
double WntConcentration<DIM>::GetCryptLength()
{
    return mCryptLength;
}

template<unsigned DIM>
void WntConcentration<DIM>::SetCryptLength(double cryptLength)
{
    assert(cryptLength > 0.0);
    if (mLengthSet==true)
    {
        EXCEPTION("Destroy has not been called");
    }

    mCryptLength = cryptLength;
    mLengthSet = true;
}

template<unsigned DIM>
WntConcentrationType WntConcentration<DIM>::GetType()
{
    return mWntType;
}

template<unsigned DIM>
void WntConcentration<DIM>::SetType(WntConcentrationType type)
{
    if (mTypeSet==true)
    {
        EXCEPTION("Destroy has not been called");
    }
    mWntType = type;
    mTypeSet = true;
}

template<unsigned DIM>
double WntConcentration<DIM>::GetWntLevel(double height)
{
    if (mWntType == NONE)
    {
        return 0.0;
    }

    // Need to call SetCryptLength first
    assert(mLengthSet);

    double wnt_level = -1.0; // Test this is changed before leaving method.

    // The first type of Wnt concentration to try
    if (mWntType==LINEAR || mWntType==RADIAL)
    {
        if ((height >= -1e-9) && (height < mWntConcentrationParameter*GetCryptLength()))
        {
            wnt_level = 1.0 - height/(mWntConcentrationParameter*GetCryptLength());
        }
        else
        {
            wnt_level = 0.0;
        }
    }

    if (mWntType==EXPONENTIAL)
    {
        if ((height >= -1e-9) && (height < GetCryptLength()))
        {
            wnt_level = exp(-height/(GetCryptLength()*mWntConcentrationParameter));
        }
        else
        {
            wnt_level = 0.0;
        }
    }

    assert(wnt_level >= 0.0);

    return wnt_level;
}

template<unsigned DIM>
c_vector<double, DIM> WntConcentration<DIM>::GetWntGradient(c_vector<double, DIM>& rLocation)
{
    c_vector<double, DIM> wnt_gradient = zero_vector<double>(DIM);

    if (mWntType!=NONE)
    {
        if (mWntType==LINEAR)
        {
            if ((rLocation[DIM-1] >= -1e-9) && (rLocation[DIM-1] < mWntConcentrationParameter*GetCryptLength()))
            {
                wnt_gradient[DIM-1] = -1.0/(mWntConcentrationParameter*GetCryptLength());
            }
        }
        else if (mWntType==RADIAL) // RADIAL Wnt concentration
        {
            double a = GetCryptProjectionParameterA();
            double b = GetCryptProjectionParameterB();
            double r = norm_2(rLocation);
            double r_critical = pow(mWntConcentrationParameter*GetCryptLength()/a, 1.0/b);

            double dwdr = 0.0;

            if (r>=-1e-9 && r<r_critical)
            {
                dwdr = -mWntConcentrationParameter*GetCryptLength()*pow(r, b-1.0)/a;
            }

            for (unsigned i=0; i<DIM; i++)
            {
                wnt_gradient[i] = rLocation[i]*dwdr/r;
            }
        }
        else
        {
            EXCEPTION("No method to calculate gradient of this Wnt type");
        }
    }
    return wnt_gradient;
}

template<unsigned DIM>
bool WntConcentration<DIM>::IsWntSetUp()
{
    bool result = false;
    if (mTypeSet && mLengthSet && mpCellPopulation!=NULL && mWntType!=NONE)
    {
        result = true;
    }
    return result;
}

template<unsigned DIM>
void WntConcentration<DIM>::SetConstantWntValueForTesting(double value)
{
    if (value < 0)
    {
        EXCEPTION("WntConcentration<DIM>::SetConstantWntValueForTesting - Wnt value for testing should be non-negative.\n");
    }
    mConstantWntValueForTesting = value;
    mUseConstantWntValueForTesting = true;
    if (!mTypeSet)
    {
        mWntType = NONE;
    }
}

template<unsigned DIM>
double WntConcentration<DIM>::GetWntConcentrationParameter()
{
    return mWntConcentrationParameter;
}

template<unsigned DIM>
void WntConcentration<DIM>::SetWntConcentrationParameter(double wntConcentrationParameter)
{
    assert(wntConcentrationParameter > 0.0);
    mWntConcentrationParameter = wntConcentrationParameter;
}

template<unsigned DIM>
double WntConcentration<DIM>::GetCryptProjectionParameterA()
{
    return mCryptProjectionParameterA;
}

template<unsigned DIM>
double WntConcentration<DIM>::GetCryptProjectionParameterB()
{
    return mCryptProjectionParameterB;
}

template<unsigned DIM>
void WntConcentration<DIM>::SetCryptProjectionParameterA(double cryptProjectionParameterA)
{
    assert(cryptProjectionParameterA >= 0.0);
    mCryptProjectionParameterA = cryptProjectionParameterA;
}

template<unsigned DIM>
void WntConcentration<DIM>::SetCryptProjectionParameterB(double cryptProjectionParameterB)
{
    assert(cryptProjectionParameterB >= 0.0);
    mCryptProjectionParameterB = cryptProjectionParameterB;
}

// Explicit instantiation

template class WntConcentration<1>;
template class WntConcentration<2>;
template class WntConcentration<3>;